Published in Gene on June 23, 2004
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78
Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol (2005) 2.53
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA (2005) 2.28
Prokaryotic evolution and the tree of life are two different things. Biol Direct (2009) 2.17
Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct (2012) 2.05
Darwinian evolution in the light of genomics. Nucleic Acids Res (2009) 1.92
Role of the RNA polymerase trigger loop in catalysis and pausing. Nat Struct Mol Biol (2009) 1.86
The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol (2005) 1.79
Complete structural model of Escherichia coli RNA polymerase from a hybrid approach. PLoS Biol (2010) 1.69
Molecular evolution of multisubunit RNA polymerases: sequence analysis. J Mol Biol (2009) 1.67
Rooting the tree of life by transition analyses. Biol Direct (2006) 1.66
Genome-wide molecular clock and horizontal gene transfer in bacterial evolution. J Bacteriol (2004) 1.58
Structural perspective on mutations affecting the function of multisubunit RNA polymerases. Microbiol Mol Biol Rev (2006) 1.51
Molecular evolution of multisubunit RNA polymerases: structural analysis. J Mol Biol (2009) 1.45
The last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner. Biol Direct (2008) 1.40
Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J Bacteriol (2005) 1.35
Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evol Biol (2004) 1.32
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex. Proc Natl Acad Sci U S A (2009) 1.26
The Biological Big Bang model for the major transitions in evolution. Biol Direct (2007) 1.25
Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol (2008) 1.24
Mutational analysis of the ompA promoter from Flavobacterium johnsoniae. J Bacteriol (2007) 1.24
Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms. Microbiol Mol Biol Rev (2007) 1.19
Experimental RNomics in Aquifex aeolicus: identification of small non-coding RNAs and the putative 6S RNA homolog. Nucleic Acids Res (2005) 1.08
Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series. Biol Direct (2008) 1.06
Analysis of rare genomic changes does not support the unikont-bikont phylogeny and suggests cyanobacterial symbiosis as the point of primary radiation of eukaryotes. Genome Biol Evol (2009) 1.05
Insights from the architecture of the bacterial transcription apparatus. J Struct Biol (2011) 0.95
A sigma-core interaction of the RNA polymerase holoenzyme that enhances promoter escape. EMBO J (2007) 0.95
Relative predicted protein levels of functionally associated proteins are conserved across organisms. Nucleic Acids Res (2005) 0.94
Phylogeny vs genome reshuffling: horizontal gene transfer. Indian J Microbiol (2008) 0.93
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics (2006) 0.93
Characterization of single and double inactivation strains reveals new physiological roles for group 2 sigma factors in the cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol (2008) 0.93
The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins. Nucleic Acids Res (2007) 0.89
A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes. Biol Direct (2011) 0.89
A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. Trends Biochem Sci (2016) 0.86
Asymmetrical evolution of cytochrome bd subunits. J Mol Evol (2006) 0.86
Chloroplast His-to-Asp signal transduction: a potential mechanism for plastid gene regulation in Heterosigma akashiwo (Raphidophyceae). BMC Evol Biol (2007) 0.85
The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria. Nucleic Acids Res (2014) 0.82
Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation. J Biol Chem (2012) 0.81
An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters. BMC Bioinformatics (2009) 0.81
Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biol Evol (2013) 0.80
Differences in evolutionary pressure acting within highly conserved ortholog groups. BMC Evol Biol (2008) 0.78
Cloning and expression analysis of genes encoding lytic endopeptidases L1 and L5 from Lysobacter sp. strain XL1. Appl Environ Microbiol (2012) 0.77
Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures. Nat Commun (2017) 0.77
Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly. J Virol (2016) 0.76
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol (2017) 0.76
Nitropropenyl benzodioxole, an anti-infective agent with action as a protein tyrosine phosphatase inhibitor. Open Med Chem J (2014) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (2009) 32.97
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33
Small CRISPR RNAs guide antiviral defense in prokaryotes. Science (2008) 17.79
Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol (2011) 17.11
Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science (1998) 13.64
De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41
A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct (2006) 11.31
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999) 11.30
Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (2000) 10.82
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87
Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol (2001) 8.14
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science (1999) 8.01
Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49
Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet (2002) 7.25
IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91
Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50
Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res (2002) 6.08
Regeneration of peroxiredoxins by p53-regulated sestrins, homologs of bacterial AhpD. Science (2004) 5.88
Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 5.64
Selection in the evolution of gene duplications. Genome Biol (2002) 5.58
Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95
Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol (2003) 4.70
Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68
Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39
Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet (2003) 4.39
Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28
The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14
Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10
Selection for short introns in highly expressed genes. Nat Genet (2002) 4.04
Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00
Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol (2000) 3.99
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92
Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res (2003) 3.90
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (1998) 3.83
Genome trees and the tree of life. Trends Genet (2002) 3.79
The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72
Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol (2003) 3.72
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62
Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55
'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res (2004) 3.50
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res (1999) 3.44
Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36
Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J Mol Biol (1999) 3.28
Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol (2003) 3.26
The impact of comparative genomics on our understanding of evolution. Cell (2000) 3.25
PAS: a multifunctional domain family comes to light. Curr Biol (1997) 3.20
TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol (2013) 3.18
Long intervals of stasis punctuated by bursts of positive selection in the seasonal evolution of influenza A virus. Biol Direct (2006) 3.18
Comprehensive comparative-genomic analysis of type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes. Biol Direct (2009) 3.17
Introns and the origin of nucleus-cytosol compartmentalization. Nature (2006) 3.16
Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol (2007) 3.14
Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol (2006) 3.10
One-component systems dominate signal transduction in prokaryotes. Trends Microbiol (2005) 3.09
No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol (2003) 3.07
Malaria parasite clag3 genes determine channel-mediated nutrient uptake by infected red blood cells. Cell (2011) 3.06
Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol (2003) 3.02
A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats. J Biol Chem (2008) 3.00
Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily. Genome Res (1998) 2.91
START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins. Trends Biochem Sci (1999) 2.89
Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends Genet (1999) 2.87
A universal trend of amino acid gain and loss in protein evolution. Nature (2005) 2.81
Conservation and coevolution in the scale-free human gene coexpression network. Mol Biol Evol (2004) 2.78
New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol (2003) 2.77
The U box is a modified RING finger - a common domain in ubiquitination. Curr Biol (2000) 2.73
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair. Mol Microbiol (2010) 2.70
Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol (2001) 2.68
Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol (2009) 2.66
Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins (2001) 2.65
Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res (2001) 2.65
Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle (2004) 2.65
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res (2004) 2.62
The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem Sci (2000) 2.58
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS (2006) 2.57
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct (2007) 2.53